Virtual Fly Brain—An interactive atlas of the Drosophila nervous system

Abstract

As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.

Transforming descending input into behavior: The organization of premotor circuits in theDrosophilaMale Adult Nerve Cord connectome

“…We obtained the VNC longitudinal tract meshes generated by (Court et al, 2020) from https://www.virtualflybrain.org/ (Court et al, 2023) (ids: VFB_00104642, VFB_00104635, VFB_00104636, VFB_00104637, VFB_00104634, VFB_00104638, VFB_00104633) and transformed them from their original JRC2018VNC_U space into MANC space. We then simplified all DN axon skeletons to their longest neurite starting from their VNC entrance in the neck connective and NBLAST clustered them.…”

Multiple Isoforms of the Activin-like receptor Baboon differentially regulate proliferation and conversion behaviors of neuroblasts and neuroepithelial cells in theDrosophilalarval brain

“…Postembryonic NBs in the central brain differ in their proliferation behavior before and after the CW checkpoint [7]. Prior to the CW checkpoint (i.e., first phase), NBs divide slowly and their division rate is sensitive to dietary protein contents, while NBs post CW checkpoint (second phase) divide faster in a manner independent of dietary status [16].…”

Semantic Representation of Neural Circuit Knowledge inCaenorhabditis elegans

“…One way to achieve this is by representing compiled neurobiological data in an anatomical context. For instance, the Virtual Fly Brain project has used an ontology-based approach to integrate connectivity and single-cell gene expression data, which can be visualised in a 3-dimensional visualization of the brain, using a semantic integration framework (Milyaev et al 2012; Court et al 2023). This allows users to run queries to explore gene expression and phenotype data in an anatomic context.…”